Using the divisionsCompute-serversPubH 840091714.ppt

Using the divisions Compute-servers PubH 8400 9/17/14 List of compute servers For students: potassium.biostat.umn.edu cesium.biostat.umn.edu carbon.biostat.umn.edu chromium.biostat.umn.edu For faculty: rubidium.biostat.umn.edu silicon.biostat.umn.edu All servers have 24 cores (processors) How to access servers Directly ssh in from anywhere within the umn.edu domain (U of M network) If coming from outside of umn.edu ssh to merganser.biostat.umn.edu, then ssh to the desired server Log into the University VPN and ssh directly to the desired host Server utilization - CPU days Cesium usage, June 2012 Potassium usage, June 2012 Computing etiquette Dont run open-ended jobs Estimate of the jobs duration Run a small version of the job to get estimate “nice” your jobs r within “top” “renice 19 process number” on command line Dont run too many concurrent jobs (or too many threads) on one server Monitor your jobs Use “top” Know how to kill your jobs In “top” use “k” From command line: kill process number kill -1 process number kill -9 process number (sure kill, use as last resort) Write to a file as job progresses Automatic monitoring System programs monitor each users compute-bound jobs If user runs too many compute-bound processes/threads, jobs are automatically “niced” to a lower priority Perhaps we will add annoying E-mail notifications if jobs run too many days Threaded jobs A threaded job breaks into “threads” where each thread runs independently and can run on different processors A threaded job could saturate all 24 cores “top” can tell you if a job is threading Run only 1 or 2 threaded jobs per server Serialize threaded jobs, rather than running many such jobs concurrently Using “top” q to quit 1 toggle “show all cores/show summary” Need a window with at least 36 lines H toggle “show all threads/show summary” k kill a job h help * * * * * * * * * * * * * * * * * * * * * *